Generate Measurements from Synthetic Data

Overview

Use this skill when you have a 3D ground-truth (GT) volume and want to simulate what the microscope/system would measure, using precomputed system matrices (the forward operator $A$).

This is typically a prerequisite for solver development and benchmarking:

• •GT volume ($x$): reconstruction.pt (or similar)
• •system matrices ($A$): Interp_Vol_ID_*.pt files in a directory
• •output measurements ($b = Ax$): saved as .tif images

Instructions

1. •Prepare the ground-truth volume.

• •Ensure the GT volume is a .pt file (for example reconstruction.pt).
• •If your GT is stored in H5 format, convert it using scripts/convert_h5_to_pt.py.

1. •Locate the forward model (A matrices).

• •Identify the directory containing Interp_Vol_ID_*.pt.
• •Confirm this directory corresponds to the same optical/system setup you want to simulate.

1. •Pick/verify the crop (if needed).

• •If the A volume extent is larger than your GT volume (or mismatched), set --crop-box-A.
• •Format is x0 y0 z0 x1 y1 z1
• •User would give the crop, or check crop in most related config/*.yaml. If you do not know how to crop, stop and ask user for help.

1. •(Optional) Decide on noise injection.

• •Use --noise-index to add noise to a specific measurement index.
• •Use --noise-index -1 for clean measurement without noise.

1. •Generate the measurements.

Run scripts/generate_bunny_measurements.py with:

• •--gt-vol-path: path to GT .pt
• •--raw-A-dir: path to the system matrices
• •--output-dir: output folder for .tif measurements

What success looks like

You should consider this skill successful when:

• •the script finishes without error, and
• •output_dir contains one or more .tif measurement images, and
• •(recommended) the images look plausible (non-empty, not all zeros/NaNs) when opened or visualized.

Examples

Example: generate noise-free measurements with A-cropping

Generate measurements from a GT volume using a specified system-matrix directory, and crop A to match the GT:

python scripts/generate_bunny_measurements.py \
  --gt-vol-path data/synthetic/balls/case_1/reconstruction.pt \
  --raw-A-dir data/raw/lightsheet_vol_6.9 \
  --output-dir data/synthetic/balls/case_1/measurements \
  --crop-box-A 5 268 18 69 332 82 \
  --noise-index -1